From a6c698b20eda3671d22466ab6b98b36331a30804 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Wed, 3 Jun 2009 18:39:56 +0000
Subject: [PATCH] fixed a bug in calculating the # of ambig bases

---
 sequence.cpp | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sequence.cpp b/sequence.cpp
index 423b905..e9487c5 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -75,8 +75,8 @@ void Sequence::initialize(){
 	isAligned = 0;
 	startPos = -1;
 	endPos = -1;
-	longHomoPolymer = 0;
-	ambigBases = 0;
+	longHomoPolymer = -1;
+	ambigBases = -1;
 	
 }	
 
@@ -212,7 +212,7 @@ int Sequence::getAlignLength(){
 
 int Sequence::getAmbigBases(){
 	if(ambigBases == -1){
-	
+		ambigBases = 0;
 		for(int j=0;j<numBases;j++){
 			if(unaligned[j] != 'A' && unaligned[j] != 'T' && unaligned[j] != 'G' && unaligned[j] != 'C'){
 				ambigBases++;
@@ -226,8 +226,8 @@ int Sequence::getAmbigBases(){
 //********************************************************************************************************************
 
 int Sequence::getLongHomoPolymer(){
-	if(longHomoPolymer == 0){
-
+	if(longHomoPolymer == -1){
+		longHomoPolymer = 1;
 		int homoPolymer = 1;
 		for(int j=1;j<numBases;j++){
 			if(unaligned[j] == unaligned[j-1]){
-- 
2.39.2